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tests.yml
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name: tests
on:
push:
schedule:
- cron: "0 0 * * 0" # weekly
env:
CONDA_PKGS_DIRS: /home/runner/pkgs
jobs:
test_models:
runs-on: ubuntu-latest
strategy:
fail-fast: false
steps:
- uses: actions/checkout@v3
with:
submodules: recursive
- name: Setup conda
uses: s-weigand/[email protected]
with:
update-conda: true
python-version: 3.7
conda-channels: anaconda, conda-forge, bioconda
- name: Create environment
run: |
conda install -n base mamba -c conda-forge
conda clean --all -y
mamba env create -f environment.yml
- name: Run tests with pytest
run: |
source activate metamers
pytest tests/test_models.py
test_snakefile:
runs-on: ubuntu-latest
strategy:
fail-fast: false
steps:
- uses: actions/checkout@v3
with:
submodules: recursive
- name: Setup conda
uses: s-weigand/[email protected]
with:
update-conda: true
python-version: 3.7
conda-channels: anaconda, conda-forge, bioconda
- name: Create environment
run: |
conda install -n base mamba
conda clean --all -y
mamba env create -f environment.yml
- name: Setup FFmpeg
uses: FedericoCarboni/setup-ffmpeg@v2
- name: Download data
run: |
mkdir -p data/metamers/ref_images/
curl -O -J -L https://osf.io/4wyg3/download
tar xf textures-subset-for-testing.tar.gz -C data
rm textures-subset-for-testing.tar.gz
- name: modify config.yml
run: |
sed -i 's|DATA_DIR:.*|DATA_DIR: "data/metamers"|g' config.yml
sed -i 's|TEXTURE_DIR:.*|TEXTURE_DIR: "data/textures-subset-for-testing"|g' config.yml
- name: run snakemake test
run: |
source activate metamers
cp extra_packages/data/einstein.pgm data/metamers/ref_images/einstein_size-256,256.png
snakemake -j 5 -prk data/metamers/test_setup/RGC_norm_gaussian_gpu-0/einstein data/metamers/test_setup/V1_norm_s6_gaussian_gpu-0/einstein
run_Freeman_check_notebook:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
submodules: recursive
- name: Setup conda
uses: s-weigand/[email protected]
with:
update-conda: true
python-version: 3.7
conda-channels: anaconda, conda-forge, bioconda
- name: Create environment
run: |
conda install -n base mamba
conda clean --all -y
mamba env create -f environment.yml
source activate metamers
mamba install jupyter nbclient>=0.5.5
- name: modify config.yml
run: |
sed -i 's|DATA_DIR:.*|DATA_DIR: "data/metamers"|g' config.yml
sed -i 's|TEXTURE_DIR:.*|TEXTURE_DIR: "data/textures-subset-for-testing"|g' config.yml
mkdir -p data/metamers
mkdir -p data/textures-subset-for-testing
- name: Download data
run : |
source activate metamers
python download_data.py freeman2011_check_output -s
python download_data.py freeman2011_check_input -s
- name: run nbconvert
run: |
source activate metamers
jupyter execute notebooks/Freeman_Check.ipynb --kernel_name=python3
test_mcmc:
runs-on: ubuntu-latest
strategy:
fail-fast: false
steps:
- uses: actions/checkout@v3
with:
submodules: recursive
- name: Setup conda
uses: s-weigand/[email protected]
with:
update-conda: true
python-version: 3.7
conda-channels: anaconda, conda-forge, bioconda
- name: Create environment
run: |
conda install -n base mamba
conda clean --all -y
mamba env create -f environment.yml
- name: modify config.yml
run: |
sed -i 's|DATA_DIR:.*|DATA_DIR: "data/metamers"|g' config.yml
sed -i 's|TEXTURE_DIR:.*|TEXTURE_DIR: "data/textures-subset-for-testing"|g' config.yml
mkdir -p data/metamers
mkdir -p data/textures-subset-for-testing
- name: Download data
run: |
source activate metamers
python download_data.py behavioral_data -s
- name: run mcmc test
run: |
source activate metamers
# test one that has a single subject, one with multiple
snakemake -j 5 -prk data/metamers/mcmc/V1_norm_s6_gaussian/task-split_comp-ref/task-split_comp-ref_mcmc_partially-pooled_step-1_prob-.8_depth-10_c-2_d-10_w-10_s-0.nc data/metamers/mcmc/V1_norm_s6_gaussian/task-split_comp-ref-natural/task-split_comp-ref-natural_mcmc_partially-pooled_step-1_prob-.8_depth-10_c-2_d-10_w-10_s-0.nc